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comparison stacks_sstacks.xml @ 3:344cfdb7dd48 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:28:25 -0400
parents 17469af4e858
children 679f97ac0dd5
comparison
equal deleted inserted replaced
2:e880ddd2d8fa 3:344cfdb7dd48
1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1">
2 <description>match stacks to a catalog</description> 2 <description>match stacks to a catalog</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
12 12
13 && 13 &&
14 14
15 #set $catalog = "" 15 #set $catalog = ""
16 #for $input_file in $input_cat: 16 #for $input_file in $input_cat:
17 #set $filename = str($input_file.name) 17 #set $filename = str($input_file.element_identifier)
18 #if not filename.endswith('.tsv'): 18 #if not filename.endswith('.tsv'):
19 #set $filename = ".tsv" 19 #set $filename = $filename + ".tsv"
20 #end if 20 #end if
21 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename): 21 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
22 ln -s "${input_file}" "stacks_inputs/$filename" && 22 ln -s "${input_file}" "stacks_inputs/$filename" &&
23 23
24 #if $filename.endswith('.tags.tsv'): 24 #if $filename.endswith('.tags.tsv'):
27 #end if 27 #end if
28 #end for 28 #end for
29 29
30 #set $samples = "" 30 #set $samples = ""
31 #for $input_file in $input_tags: 31 #for $input_file in $input_tags:
32 #set $filename = str($input_file.name) 32 #set $filename = str($input_file.element_identifier)
33 #if not filename.endswith('.tsv'): 33 #if not filename.endswith('.tsv'):
34 #set $filename = ".tsv" 34 #set $filename = $filename + ".tsv"
35 #end if 35 #end if
36 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename): 36 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
37 ln -s "${input_file}" "stacks_inputs/$filename" && 37 ln -s "${input_file}" "stacks_inputs/$filename" &&
38 38
39 #if $filename.endswith('.tags.tsv'): 39 #if $filename.endswith('.tags.tsv'):
58 $check_haplo 58 $check_haplo
59 59
60 $gapped 60 $gapped
61 61
62 -o stacks_outputs 62 -o stacks_outputs
63
64 > sstacks.log 2>&1
63 ]]></command> 65 ]]></command>
64 66
65 <inputs> 67 <inputs>
66 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> 68 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
67 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" /> 69 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" />
72 74
73 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> 75 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
74 </inputs> 76 </inputs>
75 77
76 <outputs> 78 <outputs>
79 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
80
77 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> 81 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
78 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" /> 82 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
79 </collection> 83 </collection>
80 </outputs> 84 </outputs>
81 85
82 <tests> 86 <tests>
83 <test> 87 <test>
99 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> 103 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
100 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> 104 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
101 </collection> 105 </collection>
102 </param> 106 </param>
103 107
108 <output name="output_log">
109 <assert_contents>
110 <has_text text="Outputing to file" />
111 </assert_contents>
112 </output>
113
104 <output_collection name="matches"> 114 <output_collection name="matches">
105 <element name="PopA_01.matches"> 115 <element name="PopA_01.matches">
106 <assert_contents> 116 <assert_contents>
107 <has_text text="generated on " /> 117 <has_text text="generated on " />
108 </assert_contents> 118 </assert_contents>
130 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> 140 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
131 </collection> 141 </collection>
132 </param> 142 </param>
133 <param name="gapped" value="true" /> 143 <param name="gapped" value="true" />
134 <param name="check_haplo" value="true" /> 144 <param name="check_haplo" value="true" />
145
146 <output name="output_log">
147 <assert_contents>
148 <has_text text="Outputing to file" />
149 </assert_contents>
150 </output>
135 151
136 <output_collection name="matches"> 152 <output_collection name="matches">
137 <element name="PopA_01.matches"> 153 <element name="PopA_01.matches">
138 <assert_contents> 154 <assert_contents>
139 <has_text text="generated on " /> 155 <has_text text="generated on " />